Given that your data file has thousands of lines you may be better choosing a different approach. I assume that end is always lower case. Set the input record separator to $/ = "\nend\n". Now each read of a file reads in a paragraph terminated by an end by itself on a line. The advantage is that you don't need to read in the whole file to memory and it should scale better.

local $/ = "\nend\n";
while ( my $data = <DATA> ) {
    $data =~ s/^.*start/start/is;
    print $data;
    print '=' x 10, "\n";
}

__DATA__
start
start
start
go
one
end
start
start
start
go
two
end
[download]

start
go
one
end
==========
start
go
two
end
==========
[download]

If my assumption of a lower case end is incorrect then you can achieve the same effect with

my $data = '';
while ( my $line = <DATA> ) {
    $data .= $line;
    if ( $line =~ /^end$/i ) {
        $data =~ s/^.*start/start/is;
        print $data;
        print '=' x 10, "\n";
        $data = '';
    }
}
[download]